Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a global infectious disease emergency. A major hurdle in combating TB is the fact Mtb is able to persist for long periods of time in host tissues, in a quiescent state. These bacilli are able to reactivate and cause pulmonary TB, when the immune system is compromised. Hence, a complete understanding of TB latency and reactivation is required for the effective control of TB. The research models and tools necessary to perform these studies are now available. Nonhuman Primates (NHPs) are excellent models of TB, especially to study the progression of experimental infection to latency, and to study the pathology and biology of granulomatous lesions - the hallmarks of TB infections. We have established a model of human TB, by exposing NHPs to true Mtb aerosols. While many research groups focus on the bacterial factors of latency and reactivation, we would like to leverage our highly tractable model to identify host signatures and mediators of this process. We show that pro-inflammatory immune signaling pathways, initially induced in NHP TB lesions, are overwhelmingly silenced over the course of next several weeks. This transcriptional reprogramming could be a host response to changes in bacterial replication and physiology. Further, these responses could reflect the efforts of the pathogen to prevent excessive immunopathology during the infection of lungs. The central hypothesis of our proposal is that host granuloma responses can be used to predict latent and reactivation TB. We propose to perform a systematic study of the transcriptome and the miRNAome of NHP lung lesions. Temporal profiles will be obtained from NHPs infected with a low-dose of Mtb aerosols, accurately modeling long-term latent infection. Profiles will also be obtained from NHPs in which latent TB is reactivated by simian AIDS. These system-wide profiles, in conjugation with the clinical, microbiological and immunological data obtained from infected NHPs will generate statistical learning algorithms and mixed effects computational models of latent and reactivation TB. The relevance of some of the most informative set of genetic predictors available from the data collected will be tested back in both the NHP model, as well as in human patients. The expression profiles of CCL24, CCL25 and CCL27 show negative correlation with all other chemokine ligands and receptors in primate TB granulomas. The expression of these three chemokines is significantly increased in late, rather than early lesions. We hypothesize that these chemokines are important for the long-term maintenance of primate lesions harboring latent Mtb bacilli. The expression of LAG3 was induced more than 40-fold in early primate lesions relative to late ones. LAG3 is a novel marker of Treg cells. We hypothesize that LAG3 is responsible for negatively regulating protective immune responses generated by effector T cells in primate TB lesions. The expression of latency specific genes CCL24/25/27 and the active-TB: specific gene LAG3 will be silenced in NHPs using a novel lipidated-siRNA nanoparticle based approach. The progression of latent disease and its immunological and molecular correlates will then be studied in these animals. Finally, the expression of an immune response to these and other latency and reactivation- specific profiles will be determined in human patients of latent and active TB, as well as TB/AIDS co- infected patients. These systems-biology studies will likely exponentially enhance our understanding of TB latency and reactivation in a host that mimics both TB and AIDS in the closest possible manner to humans. Eventually, these advances may empower clinicians better to detect and treat latent TB.